applications/staticProps/NanoVolume.cpp

/* Copyright (c) 2006, 2009, 2010 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 *
 *
 *  NanoVolume.cpp
 *
 *  Created by Charles F. Vardeman II on 14 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: NanoVolume.cpp,v 1.10 2009-11-25 20:01:59 gezelter Exp $
 *
 */

#include "applications/staticProps/NanoVolume.hpp"
#include "math/ConvexHull.hpp"
#include "math/AlphaHull.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"

using namespace OpenMD;

NanoVolume::NanoVolume(SimInfo* info,
                       const std::string& filename,
                       const std::string& sele)
  : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) {
  setOutputName(getPrefix(filename) + ".avol");
  
  evaluator_.loadScriptString(sele);
  if (!evaluator_.isDynamic()) {
    seleMan_.setSelectionSet(evaluator_.evaluate());
  }
  frameCounter_ = 0;
  totalVolume_ = 0.0;
}

void NanoVolume::process() {
#if defined(HAVE_QHULL)
  Molecule* mol;
  Atom* atom;
  RigidBody* rb;
  int myIndex;
  SimInfo::MoleculeIterator mi;
  Molecule::RigidBodyIterator rbIter;
  Molecule::AtomIterator ai;
  StuntDouble* sd;
  Vector3d vec;
  int i,j;

#ifdef HAVE_QHULL
  // ConvexHull* thishull = new ConvexHull();
  AlphaHull* thishull = new AlphaHull(2.0);
#endif

  DumpReader reader(info_, dumpFilename_);
  int nFrames = reader.getNFrames();
  frameCounter_ = 0;

  theAtoms_.reserve(info_->getNGlobalAtoms());

  for (int istep = 0; istep < nFrames; istep += step_) {
    reader.readFrame(istep);
    frameCounter_++;
    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    
    // Clear pos vector between each frame.
    theAtoms_.clear();
    
    if (evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
    
    // update the positions of atoms which belong to the rigidbodies
    
    for (mol = info_->beginMolecule(mi); mol != NULL;
         mol = info_->nextMolecule(mi)) {
      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
           rb = mol->nextRigidBody(rbIter)) {   
        rb->updateAtoms();
      }
    }
    
    // outer loop is over the selected StuntDoubles:
    
    for (sd = seleMan_.beginSelected(i); sd != NULL;
            sd = seleMan_.nextSelected(i)) {
      
     theAtoms_.push_back(sd);
      myIndex = sd->getGlobalIndex();
      
    }
    
    /*
    for (mol = info_->beginMolecule(mi); mol != NULL; 
                 mol = info_->nextMolecule(mi)) {
              for (atom = mol->beginAtom(ai); atom != NULL; 
                   atom = mol->nextAtom(ai)) {
                     theAtoms_.push_back(atom);
              }
            }
    */
    // Generate convex hull for this frame.
    thishull->computeHull(theAtoms_);
  //  totalVolume_ += hull->getVolume();                
  }
  //RealType avgVolume = totalVolume_/(RealType) frameCounter_;
  //std::cout.precision(7);
  //std::cout  << avgVolume << std::endl;
/*
  std::ofstream osq(getOutputFileName().c_str());
  osq.precision(7);
  if (osq.is_open()){
      osq << avgVolume << std::endl;

  }
  osq.close();
*/
#else
  sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n");
  painCave.isFatal = 1;
  simError();  

#endif

}
Revision:	1402
Committed:	Fri Jan 8 17:15:27 2010 UTC (15 years, 3 months ago) by chuckv
File size:	5332 byte(s)
Log Message:	Added preliminary code for Alpha Hull calculation using qhull. Added preliminary support to SMIPD to support Alpha Hull. Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. Preliminary changes for shadow hamiltonian integrator. Chages to md files so they will work in openMD.
#	User	Rev	Content
1	chuckv	1402	/* Copyright (c) 2006, 2009, 2010 The University of Notre Dame. All Rights Reserved.
2	chuckv	1181	*
3			* The University of Notre Dame grants you ("Licensee") a
4			* non-exclusive, royalty free, license to use, modify and
5			* redistribute this software in source and binary code form, provided
6			* that the following conditions are met:
7			*
8	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
9	chuckv	1181	* notice, this list of conditions and the following disclaimer.
10			*
11	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
12	chuckv	1181	* notice, this list of conditions and the following disclaimer in the
13			* documentation and/or other materials provided with the
14			* distribution.
15			*
16			* This software is provided "AS IS," without a warranty of any
17			* kind. All express or implied conditions, representations and
18			* warranties, including any implied warranty of merchantability,
19			* fitness for a particular purpose or non-infringement, are hereby
20			* excluded. The University of Notre Dame and its licensors shall not
21			* be liable for any damages suffered by licensee as a result of
22			* using, modifying or distributing the software or its
23			* derivatives. In no event will the University of Notre Dame or its
24			* licensors be liable for any lost revenue, profit or data, or for
25			* direct, indirect, special, consequential, incidental or punitive
26			* damages, however caused and regardless of the theory of liability,
27			* arising out of the use of or inability to use software, even if the
28			* University of Notre Dame has been advised of the possibility of
29			* such damages.
30			*
31	gezelter	1390	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32			* research, please cite the appropriate papers when you publish your
33			* work. Good starting points are:
34			*
35			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38			* [4] Vardeman & Gezelter, in progress (2009).
39	chuckv	1181	*
40	gezelter	1390	*
41	chuckv	1181	* NanoVolume.cpp
42			*
43			* Created by Charles F. Vardeman II on 14 Dec 2006.
44			* @author Charles F. Vardeman II
45	gezelter	1390	* @version $Id: NanoVolume.cpp,v 1.10 2009-11-25 20:01:59 gezelter Exp $
46	chuckv	1181	*
47			*/
48
49			#include "applications/staticProps/NanoVolume.hpp"
50			#include "math/ConvexHull.hpp"
51	chuckv	1402	#include "math/AlphaHull.hpp"
52	chuckv	1181	#include "utils/simError.h"
53			#include "io/DumpReader.hpp"
54			#include "primitives/Molecule.hpp"
55			#include "utils/NumericConstant.hpp"
56
57	gezelter	1390	using namespace OpenMD;
58	chuckv	1181
59			NanoVolume::NanoVolume(SimInfo* info,
60			const std::string& filename,
61			const std::string& sele)
62			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) {
63	chuckv	1194	setOutputName(getPrefix(filename) + ".avol");
64	chuckv	1181
65			evaluator_.loadScriptString(sele);
66			if (!evaluator_.isDynamic()) {
67			seleMan_.setSelectionSet(evaluator_.evaluate());
68			}
69	chuckv	1188	frameCounter_ = 0;
70			totalVolume_ = 0.0;
71	chuckv	1181	}
72
73			void NanoVolume::process() {
74	gezelter	1382	#if defined(HAVE_QHULL)
75	chuckv	1181	Molecule* mol;
76			Atom* atom;
77			RigidBody* rb;
78			int myIndex;
79			SimInfo::MoleculeIterator mi;
80			Molecule::RigidBodyIterator rbIter;
81			Molecule::AtomIterator ai;
82			StuntDouble* sd;
83			Vector3d vec;
84			int i,j;
85
86	chuckv	1199	#ifdef HAVE_QHULL
87	chuckv	1402	// ConvexHull* thishull = new ConvexHull();
88			AlphaHull* thishull = new AlphaHull(2.0);
89	chuckv	1199	#endif
90	chuckv	1181
91			DumpReader reader(info_, dumpFilename_);
92			int nFrames = reader.getNFrames();
93			frameCounter_ = 0;
94
95	chuckv	1293	theAtoms_.reserve(info_->getNGlobalAtoms());
96	chuckv	1181
97			for (int istep = 0; istep < nFrames; istep += step_) {
98			reader.readFrame(istep);
99			frameCounter_++;
100			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
101
102			// Clear pos vector between each frame.
103	chuckv	1293	theAtoms_.clear();
104	chuckv	1181
105			if (evaluator_.isDynamic()) {
106			seleMan_.setSelectionSet(evaluator_.evaluate());
107			}
108
109			// update the positions of atoms which belong to the rigidbodies
110
111			for (mol = info_->beginMolecule(mi); mol != NULL;
112			mol = info_->nextMolecule(mi)) {
113			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
114			rb = mol->nextRigidBody(rbIter)) {
115			rb->updateAtoms();
116			}
117			}
118
119			// outer loop is over the selected StuntDoubles:
120	chuckv	1304
121	chuckv	1181	for (sd = seleMan_.beginSelected(i); sd != NULL;
122	chuckv	1293	sd = seleMan_.nextSelected(i)) {
123	chuckv	1181
124	chuckv	1304	theAtoms_.push_back(sd);
125	chuckv	1181	myIndex = sd->getGlobalIndex();
126
127			}
128	chuckv	1304
129			/*
130	chuckv	1293	for (mol = info_->beginMolecule(mi); mol != NULL;
131			mol = info_->nextMolecule(mi)) {
132			for (atom = mol->beginAtom(ai); atom != NULL;
133			atom = mol->nextAtom(ai)) {
134			theAtoms_.push_back(atom);
135			}
136			}
137	chuckv	1304	*/
138	chuckv	1181	// Generate convex hull for this frame.
139	chuckv	1293	thishull->computeHull(theAtoms_);
140	chuckv	1207	// totalVolume_ += hull->getVolume();
141	chuckv	1181	}
142	chuckv	1207	//RealType avgVolume = totalVolume_/(RealType) frameCounter_;
143	chuckv	1194	//std::cout.precision(7);
144			//std::cout << avgVolume << std::endl;
145	chuckv	1207	/*
146	chuckv	1194	std::ofstream osq(getOutputFileName().c_str());
147			osq.precision(7);
148			if (osq.is_open()){
149			osq << avgVolume << std::endl;
150
151			}
152			osq.close();
153	chuckv	1207	*/
154	cpuglis	1195	#else
155	gezelter	1382	sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n");
156	cpuglis	1195	painCave.isFatal = 1;
157			simError();
158	chuckv	1207
159	cpuglis	1195	#endif
160	chuckv	1207
161	chuckv	1181	}